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https://www.readbyqxmd.com/read/28213793/automation-of-peak-tracking-analysis-of-stepwise-perturbed-nmr-spectra
#1
Tommaso Banelli, Marco Vuano, Federico Fogolari, Andrea Fusiello, Gennaro Esposito, Alessandra Corazza
We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered...
February 17, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28213211/application-of-2d-hplc-coupled-with-principal-component-analysis-to-study-an-industrial-opiate-processing-stream
#2
Paul G Stevenson, Niki K Burns, Stuart D Purcell, Paul S Francis, Neil W Barnett, Fiona Fry, Xavier A Conlan
Principal component analysis (PCA) loading plots were used to elucidate key differences between two-dimensional high performance liquid chromatography (2D-HPLC) fingerprint data from samples collected from stages along the Papaver somniferum industrial process chemistry workflow. Data reduction was completed using a 2D-HPLC peak picking approach as a precursor to chemometric analysis. Using comparisons of the final stages of product extraction as an example, PCA analysis of characteristic 2D-HPLC fingerprints accounted for 84...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28160196/infos-spectrum-fitting-software-for-nmr-analysis
#3
Albert A Smith
Software for fitting of NMR spectra in MATLAB is presented. Spectra are fitted in the frequency domain, using Fourier transformed lineshapes, which are derived using the experimental acquisition and processing parameters. This yields more accurate fits compared to common fitting methods that use Lorentzian or Gaussian functions. Furthermore, a very time-efficient algorithm for calculating and fitting spectra has been developed. The software also performs initial peak picking, followed by subsequent fitting and refinement of the peak list, by iteratively adding and removing peaks to improve the overall fit...
February 3, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28160195/peak-picking-multidimensional-nmr-spectra-with-the-contour-geometry-based-algorithm-cypick
#4
Julia M Würz, Peter Güntert
The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity...
February 3, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28150425/integrated-hptlc-based-methodology-for-the-tracing-of-bioactive-compounds-in-herbal-extracts-employing-multivariate-chemometrics-a-case-study-on-morus-alba
#5
Eliza Chaita, Evagelos Gikas, Nektarios Aligiannis
INTRODUCTION: In drug discovery, bioassay-guided isolation is a well-established procedure, and still the basic approach for the discovery of natural products with desired biological properties. However, in these procedures, the most laborious and time-consuming step is the isolation of the bioactive constituents. A prior identification of the compounds that contribute to the demonstrated activity of the fractions would enable the selection of proper chromatographic techniques and lead to targeted isolation...
February 2, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28012801/occurrence-and-variation-of-lipophilic-shellfish-toxins-in-phytoplankton-shellfish-and-seawater-samples-from-the-aquaculture-zone-in-the-yellow-sea-china
#6
Meihui Li, Geng Sun, Jiangbing Qiu, Aifeng Li
Lipophilic shellfish toxins (LSTs) produced by diverse microalgae have become a potential threat to the marine aquaculture industry in coastal regions throughout the world. In this study, phytoplankton, scallop, and seawater samples were collected and monitored in the aquaculture zone of Liuqing Bay located in the coast of Qingdao, Yellow Sea, in 2014 and 2015. Dissolved LSTs in seawater were adsorbed by solid phase adsorption toxin tracking (SPATT) bags and solid phase extraction (SPE) cartridges, respectively...
December 22, 2016: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/27966901/multiplexed-post-experimental-monoisotopic-mass-refinement-mpe-mmr-to-increase-sensitivity-and-accuracy-in-peptide-identifications-from-tandem-mass-spectra-of-cofragmentation
#7
Inamul Hasan Madar, Seung-Ik Ko, Hokeun Kim, Dong-Gi Mun, Sangtae Kim, Richard D Smith, Sang-Won Lee
Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation...
December 22, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27924495/autopiquer-a-robust-and-reliable-peak-detection-algorithm-for-mass-spectrometry
#8
David P A Kilgour, Sam Hughes, Samantha L Kilgour, C Logan Mackay, Magnus Palmblad, Bao Quoc Tran, Young Ah Goo, Robert K Ernst, David J Clarke, David R Goodlett
We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible...
December 6, 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27908224/serum-substance-p-concentrations-to-predict-oocyte-maturation-index-and-clinical-pregnancy
#9
Yavuz Sahin, Enis Özkaya, Semra Kayatas Eser, Tayfun Kutlu, Ilhan Sanverdi, Gulden Tunali, Ates Karateke
AIM: The aim of this study was to assess the predictive value of serum substance P (SP) concentrations on oocyte maturation and clinical pregnancy. METHODS: Ninety-three women with unexplained infertility underwent intracytoplasmic sperm injection (ICSI) cycles. Antagonist protocol was started for each participant and at the day of oocyte pick up, serum samples were obtained from each participant to assess SP concentrations, and these concentrations were utilized to predict mature/total oocyte ratio and clinical pregnancy...
December 2, 2016: Gynecological Endocrinology
https://www.readbyqxmd.com/read/27900236/identification-of-two-sulfated-cholesterol-metabolites-found-in-the-urine-of-a-patient-with-niemann-pick-disease-type-c-as-novel-candidate-diagnostic-markers
#10
Masamitsu Maekawa, Kaoru Omura, Shoutaro Sekiguchi, Takashi Iida, Daisuke Saigusa, Hiroaki Yamaguchi, Nariyasu Mano
In the urine of a Niemann-Pick disease type C (NPC) patient, we have identified three characteristic intense peaks that have not been observed in the urine of a 3β-hydroxysteroid-Δ(5)-C27-steroid dehydrogenase deficiency patient or a healthy infant and adult. Based on accurate masses of the protonated molecules, we focused on two of them as candidate NPC diagnostic markers. Two synthesized authentic preparations agreed with the two compounds found in NPC patient urine in regard to both chromatographic behavior and accurate masses of the deprotonated molecules...
2016: Mass Spectrometry
https://www.readbyqxmd.com/read/27865939/c-reactive-protein-response-is-higher-in-early-than-in-late-ovarian-hyperstimulation-syndrome
#11
Kati V M Korhonen, Hanna M Savolainen-Peltonen, Tomi S Mikkola, Aila E Tiitinen, Leila S Unkila-Kallio
OBJECTIVES: Many in vitro fertilization (IVF) complications are inflammatory by nature, some of which are even life-threatening. We evaluated the response of C-reactive protein (CRP) in IVF complications, especially in early and late ovarian hyperstimulation syndrome (OHSS), to support clinical decision making in gynecological emergency policlinics. STUDY DESIGN: In a prospective two-year study at Helsinki University Hospital, Finland, we recruited patients with IVF complications including moderate or severe OHSS (n=47 patients: 36 early and 14 late OHSS cases), or other IVF complications (n=13)...
December 2016: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/27853180/piezoelectric-extraction-of-ecg-signal
#12
Mahmoud Al Ahmad
The monitoring and early detection of abnormalities or variations in the cardiac cycle functionality are very critical practices and have significant impact on the prevention of heart diseases and their associated complications. Currently, in the field of biomedical engineering, there is a growing need for devices capable of measuring and monitoring a wide range of cardiac cycle parameters continuously, effectively and on a real-time basis using easily accessible and reusable probes. In this paper, the revolutionary generation and extraction of the corresponding ECG signal using a piezoelectric transducer as alternative for the ECG will be discussed...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27746230/quantitative-evaluation-of-orofacial-motor-function-in-mice-the-pasta-gnawing-test-a-voluntary-and-stress-free-behavior-test
#13
R Rabl, A Horvath, C Breitschaedel, S Flunkert, H Roemer, B Hutter-Paier
BACKGROUND: Evaluation of motor deficits in rodents is mostly restricted to limb motor tests that are often high stressors for the animals. NEW METHOD: To test rodents for orofacial motor impairments in a stress-free environment, we established the pasta gnawing test by measuring the biting noise of mice that eat a piece of spaghetti. Two parameters were evaluated, the biting speed and the biting peaks per biting episode. To evaluate the power of this test compared to commonly used limb motor and muscle strength tests, three mouse models of Parkinson's disease, amyotrophic lateral sclerosis and Niemann-Pick disease were tested in the pasta gnawing test, RotaRod and wire suspension test...
December 1, 2016: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27584561/automated-annotation-and-evaluation-of-in-source-mass-spectra-in-gc-atmospheric-pressure-chemical-ionization-ms-based-metabolomics
#14
Carsten Jaeger, Friederike Hoffmann, Clemens A Schmitt, Jan Lisec
Gas chromatography using atmospheric pressure chemical ionization coupled to mass spectrometry (GC/APCI-MS) is an emerging metabolomics platform, providing much-enhanced capabilities for structural mass spectrometry as compared to traditional electron ionization (EI)-based techniques. To exploit the potential of GC/APCI-MS for more comprehensive metabolite annotation, a major bottleneck in metabolomics, we here present the novel R-based tool InterpretMSSpectrum assisting in the common task of annotating and evaluating in-source mass spectra as obtained from typical full-scan experiments...
October 4, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27584001/erah-a-computational-tool-integrating-spectral-deconvolution-and-alignment-with-quantification-and-identification-of-metabolites-in-gc-ms-based-metabolomics
#15
Xavier Domingo-Almenara, Jesus Brezmes, Maria Vinaixa, Sara Samino, Noelia Ramirez, Marta Ramon-Krauel, Carles Lerin, Marta Díaz, Lourdes Ibáñez, Xavier Correig, Alexandre Perera-Lluna, Oscar Yanes
Gas chromatography coupled to mass spectrometry (GC/MS) has been a long-standing approach used for identifying small molecules due to the highly reproducible ionization process of electron impact ionization (EI). However, the use of GC-EI MS in untargeted metabolomics produces large and complex data sets characterized by coeluting compounds and extensive fragmentation of molecular ions caused by the hard electron ionization. In order to identify and extract quantitative information on metabolites across multiple biological samples, integrated computational workflows for data processing are needed...
October 4, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27566348/screening-halogenated-environmental-contaminants-in-biota-based-on-isotopic-pattern-and-mass-defect-provided-by-high-resolution-mass-spectrometry-profiling
#16
Ronan Cariou, Elsa Omer, Alexis Léon, Gaud Dervilly-Pinel, Bruno Le Bizec
In the present work, we addressed the question of global seeking/screening organohalogenated compounds in a large panel of complex biological matrices, with a particular focus on unknown chemicals that may be considered as potential emerging hazards. A fishing strategy was developed based on untargeted profiling among full scan acquisition datasets provided by high resolution mass spectrometry. Since large datasets arise from such profiling, filtering useful information stands as a central question. In this way, we took advantage of the exact mass differences between Cl and Br isotopes...
September 14, 2016: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27508243/dataset-and-standard-operating-procedure-for-newborn-screening-of-six-lysosomal-storage-diseases-by-tandem-mass-spectrometry
#17
Susan Elliott, Norman Buroker, Jason J Cournoyer, Anna M Potier, Joseph D Trometer, Carole Elbin, Mack J Schermer, Jaana Kantola, Aaron Boyce, Frantisek Turecek, Michael H Gelb, C Ronald Scott
In this data article we provide a detailed standard operating procedure for performing a tandem mass spectrometry, multiplex assay of 6 lysosomal enzymes for newborn screening of the lysosomal storage diseases Mucopolysaccharidosis-I, Pompe, Fabry, Niemann-Pick-A/B, Gaucher, and Krabbe, (Elliott, et al., 2016) [1]. We also provide the mass spectrometry peak areas for the product and internal standard ions typically observed with a dried blood spot punch from a random newborn, and we provide the daily variation of the daily mean activities for all 6 enzymes...
September 2016: Data in Brief
https://www.readbyqxmd.com/read/27500473/instrumental-idiosyncrasies-affecting-the-performance-of-ultrafast-chiral-and-achiral-sub-supercritical-fluid-chromatography
#18
Chandan L Barhate, M Farooq Wahab, D J Tognarelli, Terry A Berger, Daniel W Armstrong
It is widely accepted that column technology is ahead of existing chromatographic instruments. The chromatographic output may not reflect the true picture of the peak profile inside the column. The instrumental optimization parameters become far more important when peaks elute in a few seconds. In this work, the low viscosity advantage of the supercritical/subcritical CO2 is coupled with the high efficiency of narrow particle size distribution silica. Using short efficient columns and high flow rates (up to 19 mL/min), separations on the order of a few seconds are demonstrated...
September 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27479329/tric-an-automated-alignment-strategy-for-reproducible-protein-quantification-in-targeted-proteomics
#19
Hannes L Röst, Yansheng Liu, Giuseppe D'Agostino, Matteo Zanella, Pedro Navarro, George Rosenberger, Ben C Collins, Ludovic Gillet, Giuseppe Testa, Lars Malmström, Ruedi Aebersold
Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics...
September 2016: Nature Methods
https://www.readbyqxmd.com/read/27458657/binding-isotherms-and-time-courses-readily-from-magnetic-resonance
#20
Jia Xu, Steven R Van Doren
Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins...
August 16, 2016: Analytical Chemistry
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